Category Archives: Science

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Cells & Genetic Changes

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Cells can adjust and change their DNA in marvelous ways. We will look at five ways the cells adjust on a genetic level to survive. These five ways are

  • Transposition
  • Horizontal gene transfer
  • Epigenetics
  • Symbiogenesis
  • Hybridization

Transposition

Transposition is the process of cells rearranging their DNA. This process was first discovered by Barbara McClintock. In her experiments, McClintock deliberately damaged corn DNA to inhibit reproduction. The corn would pull genetic code from other places in the chromosome to maintain the ability to reproduce. In other words, the cells would take DNA from one place and insert it into another place to maintain stability and full functioning.

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How fast transposition can take place varies. For the corn experiments of McClintock, it could happen within one generation, which was the generation with the damaged DNA. In other situations, transposition could happen within a few hours, which was found among some forms of protozoan.

The implications for this include that cells know when DNA is damaged and they know how to fix this problem using other pieces of their DNA. This requires a level of mysterious intelligence that few are willing to admit that cells have.

Horizontal gene transfer

Horizontal gene transfer is the exchange of DNA between organisms. Not only do cells have internal mechanisms to fix DNA, but they can also exchange DNA with other cells. An example of this is bacteria that are resistant to antibiotics. What sometimes happens is one bacterium figures out how to resist the drugs and share this DNA with other bacteria through horizontal gene transfer.

What this means is not only do cells manipulate their DNA but when they have success they can share this with other cells. The other cells are then able to incorporate this “foreign” code into their system and have similar results.

Epigenetics

Epigenetics is the process of turning genes on and off. This is where nature vs nurture can play a critical role in development. In one experiment with rat pups, pups licked and nurtured by the mother were better able to deal with stress. This implies that the nurturing of the mother activates genes that allow for better processing of stress.

A relatable example would be weight training. Under the stress of weights, the body is transformed. Muscles get bigger, cardio improves, etc. The changes last as long as the person continues to work out. However, even if somebody stops the “memory” of these changes remains and the person can regain a great deal of the muscle just by returning to weight training.

Therefore, not only can cells manipulate their DNA and share DNA with others, but the environment itself can cause genes to shut on and off.

Symbiogenesis

Symbiogenesis is the merging of cells to cooperate. Lichen is an example of fungus and algae working together to live. Another example is chloroplast, chloroplast is an algae embedded inside plant cells.

Living cells can essentially become “one” in an attempt to have the best success at survival. This makes light of the survival of the fittest in which nature is seen as a battlefield of competition. In reality, alliances are formed for the sake of survival.

Hybridization

Hybridization is two species mating to produce a new species. Examples include tigers and lions coming together to make a liger. Or more commonly a donkey and horse making a mule.

Hybridization is genetic change at light speed. New creatures can be developed overnight with this process. However, as mentioned previously, there is a high risk of creating a genetic dead end that cannot reproduce.

Conclusion

All of the examples here indicate that changes within organisms can happen much faster than the idea of millions of years. Gene modification happens in a self-aware way that seems to defy logic and sense.

Theories on Geological Time & Origins

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Uniformitarianism is an ideal proposed by Charles Lyell (1797-1875) that the events of the past can be explained by the processes of the present and that these processes have been constant. This position for explaining Earth is also known as Lyellism.

This post will look at theories that will try to support the position of uniformitarianism in explaining the origins of the earth within the context of a religious worldview.

Local Flood Theory

The local flood theory states that instead of a worldwide flood that destroyed all land life, there was a local flood that seemed to destroy the whole world. Given that the average person only knew their local context, it seems reasonable that when a flood came that destroyed their place of living, this was the destruction of the whole world.

The local flood theory is one of the more famous theories. However, another theory may share equal prominence, and that is the Gap Theory.

Gap Theory

Gap theory claims that there were long intervals of time in the creation story as found in the creation story of the Bible. Instead of seven literal days as claimed in the Book of Genesis, these days were long periods.

Gap theory has been a popular approach to reconciling religious views on the origin of the earth with scientific views.

A similar idea is the day/age theory which states that it was not a general gap in time but rather that the days of creation were indeterminate lengths of time used for the development of the earth. There is no currently known way to very these ideas. The real purpose was to try and reconcile secular theology with religious thought.

Less Popular Theories

Diluvium theory states that a deposit of sediment was associated with the Pleistocene era. The layer of sediment found here was named Diluvium and thus the name of the theory. This was yet another attempt to try and place geology within the context of a religious worldview.

Another lesser theory is the Tranquil Theory. This theory states that the Biblical Flood slowly rose to cover the earth and slowly resided. The gradual manner of this flood is in contrast to how floods generally behave but does explain the worldwide sediment layer.

Conclusion

The point here was not to support any of these theories presented here. Instead, the point was just to show how people have tried to connect religious thoughts on the changes in this world with scientific evidence.

Acid & Bases

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We will take a look at some simple ideas related to acid bases

Acids and bases are classified by the chemical behavior of their molecules. Acids usually have a sour taste, are covalent electrolytes, and turn litmus paper red. Citric acid is one example of an acid many of us have encountered as it is commonly found in citrus fruits such as oranges. At a technical level, acids donate a H+ ion during a chemical reaction.

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On the other hand, Bases tend to have a better taste, are slippery when mixed with water, and turn litmus paper blue. Soap is one example of the use of a base in everyday life. Bases accept an H+ ion during a chemical reaction at a technical level. When acids and bases are mixed, they generally neutralize each other and produce water as a by-product.

Most acids and bases are aqueous solutions, which means they are found in a liquid state. However, some liquids do not neatly fall into the category of acid or base. Water is an example of this, and the term used to describe this is amphoteric. This means that water will sometimes donate an H+ ion or accept an H+ ion depending on the context. For this reason, water is often added to acids/bases to dilute the concentration of either one.

Water is also considered neutral on the pH scale commonly used to identify acids and bases. The Ph scale stands for potential hydrogen scale and measures the amount of hydronium ion in the solution. Lower numbers on the pH scale indicate higher levels of hydronium.

Most fruits and vegetables are considered to have low pH, thus considered base or alkaline, and they include the following

  • Avocados
  • Persimmon
  • lentils
  • Olives, black
  • Honeydew melon
  • Mangoes, ripe
  • Honeydew

Foods that are acidic in nature include the following

  • Most dairy
  • Citrus fruits
  • Meat
  • Sweeteners
  • Alcohol

There are lots of websites that promote such things as an alkaline diet. However, this is generally highly controversial, and the experts do not seem to agree about the benefits of eating alkaline foods.

Conclusions

Understanding acids/bases and their behavior can be important, especially in everyday life. Acid and bases serve a vital role in many different substances and can be helpful or harmful depending on the context.

Gases, Pressure, & Laws

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It is common in chemistry to have to deal with gases. Naturally, scientists have uncovered various laws that describe how gases act. This post will look at concepts such as pressure and the development of various laws related to gases and pressure.

Pressure and Units

Pressure is defined as (force / area). To make this practical, scientists have found that our bodies are constantly exposed to 14.7 pounds of pressure per square inch by the air around us. Our bodies are so used to this constant external pressure that without it breathing would be difficult, if not impossible.

There are various units of measurement of pressure. The Pascal, named after Blaise Pascal, is newtons per meter square. However, Pascals are rarely used by scientists. Another common unit is standard atmospheric pressure or atm for short, which is the average amount of pressure exerted by air at sea level. As a fact, one atm is the equivalent of 101,325 pascals.

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One more unit for pressure is the torr, which is 1 /760th of an atm. In terms of measuring pressure, it is common to use a barometer, and a barometer measures pressure using millimeters of mercury or mmHg. The units on a barometer are almost the same as for the torr.

Laws Related to Gases

There are several laws related to gases. For example, Boyle’s law states an inverse relationship between pressure and volume with the assumption that temperature is constant. In other words, when the pressure goes up, the volume will go down and vice versa. Boyle’s law was developed by Robert Boyle, an Irish scientist from the 17th century.

Breathing is based on Boyle’s law. When we breathe, inhaling causes the volume of our lungs to grow, which leads to a drop in pressure. The pressure drop is what allows air to flow into the lungs. The opposite takes place when we exhale. Our lungs become smaller, raising the pressure and forcing the air out of our bodies.

Charles’s laws are somewhat of a variation on Boyle’s law. This law was developed by Jacques Charles, a French scientist of the 18th century. Charles law states that if pressure is constant, then temperature and volume are proportional. In other words, when the temperature goes up or down, then the volume will go up or down.

An interesting by-product of Charles’ law is the idea behind absolute zero. Essentially, as we lower the temperature, the volume of a gas will shrink. However, gas is made of matter, and it can’t go to zero. This implies that there is a lower limit to temperature, and this lower limit is called absolute zero and is -273.15 C.

As shown below, the combined gas law combines Boyle and Charles’ law into one equation.

(p * v) / T

Pressure times volume captures a value to describe a gas in a particular context. However, we use the equation to solve for unknown values, so it is more appropriate to show it as follows.

(p1 * v1) / T1 = (p2 * v2) / T2

Conclusion

People generally dislike pressure, but the pressure is literally needed for life, at least when it comes to gases. Thanks to the work of many excellent scientists, we have a better understanding of how gases behave in the world around us.

Solutes, Solvents, & Molality

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A solution in chemistry is a homogenous mixture of two or more substances. The substances that are found in a solution can further be broken down into two types, and these are solute and solvent. The solute is the substance(s) dissolved into a solution. A solvent is a substance into which a solute is dissolved. In other words, solutes generally disappear into solvents. An example would be pouring salt into water. The salt is the solute, and the water is the solvent, and it appears that the salt disappears when added to water.

There is a limit to how much solute can be dissolved into a solvent. The term for this is solubility. Solubility varies from substance to substance but as an example, salt has a solubility of 35.9 grams per 100 grams of water. This means that you can dissolve 35.9 grams of salt in 100 grams of water. Any more salt, and there will be no more dissolving. The technical term when a solute can no longer dissolve in a solution is saturation, and the solution is now saturated.

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Solubility is also affected by temperature. For a gas, the solubility increase as the temperature is lowered. However, the solubility of a gas increases with an increase in pressure. For solids, solubility actually increases with temperature.

Concentration

The concentration measures the amount of substance in a given volume. Concentration is measured by a unit called molarity. Molarity is the proportion of the moles of solute to the liters of solution. For example, suppose I have 150 grams of calcium nitrate, and I dissolve this into 1 liter of water. In that case, I can calculate the molarity as follows.

  1. Determine the amu of calcium nitrate
    1. This is calculated by finding the number of amu, which in this case is 164.10 amu
  2. Convert the amu to moles
    1. This is done by placing the original grams as the numerator of a fraction and the amu as the denominator, which is
    2. 150/164.10 = 0.9141 moles
  3. Use the ratio
    1. Our answer is simple it is moles to solution as shown below
    2. 0.9141 moles / 1 liter = 0.9141 M

Freezing and Boiling

A final point to mention is a term called freezing point depression. This involves mixing solutes and solutions that can change the freezing point of the substance. What is taking place is that when a solute is added to a solution, it now requires more energy to freeze the new substance. This is why salt is thrown on roads during icy days. The salt lowers the temperature at which ice can form, thus making the roads safer. However, there is a limit, and if it becomes cold enough, the salt will no longer have the desired effect.

Another factor involves the boiling point. Solutes increase the temperature that is needed for boiling to occur.

Conclusion

Solutes and solvents are among many terms used in chemistry to define the behavior of substances in a certain context. It is amazing how complex the world is and how there is always so much more that can be learned in various knowledge domains.

Moles in Chemistry

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In this post we will have a brief introduction to moles in chemistry. This fundamental concepts is a part of Stoichiometry which is another important aspect of chemistry.

In chemistry an atomic mass unit (amu) is the mass of a proton or neutron in an atom. This number has been calculated to be.

1.66 X 10-24 g

Knowing this number we can calculate how much a single atom weighs. For example, if we want to calculate the weight in grams of oxygen, we know know that helium has an atomic weight of 4. This means that

The amu cancel each other. This number becomes important because if we take the amu of 1 atom of helium (or any element) in grams and divide by the mass of one atom in grams we get the following number no mattter which element we use.

This number above is how many atoms in 4 grams of helium. This number is called Avogadro’s constant but it also referred to as a mole. Knowing this value, it is possible to calculate the mass of single mole of a molecule. For example, if we want to know the mass of a single mole of glucose we would calculate the amu as shown below.

The mass is as follows

Element# of AtomsamuTotal
Carbon 612.0172.06
Hydrogen121.0112.12
Oxygen61696
Total = 180.18 amu

This output tell us that one mole of glucose is 180.18 grams. We can use this information in other ways such as determining how many moles are in a certain number of grams of a substance. If we have 15 grams of magnesium chloride MgCl2. We can calculate how many moles are in this substance as shown below

Step 1 Calculate the amu of the molecule

Mass of MgCl2 = 24.31 amu + 2 * (35.45 amu) = 95.21 amu

Step 2 Determine Conversion Reltionship

1 Mole of MgCl2 = 95.21 grams MgCl2

Step 3 Convert from grams to Moles

We now know that there are about 0.158 moles in 15 grams of magnesium chloride. But we could take this a step further by determining how many molecules are in 15 grams of magnesium chloride as shown below

0.158 * 6.02 * 1023 = 9.84 * 1022

The first number is the number of moles in 15 grams of magnesium chloride and and the second number is one mole.

There are many variations on the calculations that were done here but this is enough to serve as an introduction.

Chemical Equations

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Chemical reactions involves the rearrangement of atoms to beget new chemicals. Often these reactions are captured succinctly in what is called a chemical equation. For example, if we want to show how carbon reacts with oxygen to make carbon dioxide we would write the follow chemical equation.

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The plus sign means “reacts with” and the arrow means “to make”. Therefore, we can write this chemical equation in English by saying

Carbon reacts with oxygen to make carbon dioxide

Chemical equations need to balance. If you look at the example above, there are the same number of atoms for each element on each side. The example above is rather simple, however, sometimes it is a little trickeier to tell if an chemical equation is balanced.

In the reaction above we have to look carefully to see if the chemical equation is balanced. Starting on the left we have 1 carbon and 4 hydrogens. Next, there is a 2 which means that we multipl everything by 2 that is next to it. In other words, we do not have 2 oxygen atoms but rather 4 (2 x 2 = 4). After the arrow, we have 1 carbon and 2 oxygen atoms and after the plus sign we have 4 hydrogen atoms (2 x 2 = 4) and 2 oxygen (2 x 1 = 2). If we line everything up you can see that this equation is balanced.

Left SideRight Side
C 1 x 1 = 1 1 x 1 = 1
H 4 x 1 = 4 2 x 2 = 4
O 2 x 2 = 4 2 + (2 x 1) = 4

There are times when you need to balance a chemical equation. This can get really challlenging but we will do a simple example below.

The chemical equation above is not balance as you can see below

Left SideRight Side
H 1 x 2 = 2 1 x 1 = 1
Cl 1 x 2 = 2 1 x 1 = 1

The table above is one process in balancing an equation. We need both sides to equal each other and the simplest way to do this is to multiple the right side by two and we get the following table.

Left SideRight Side
H 1 x 2 = 2 2 x 1 = 2
Cl 1 x 2 = 2 2 x 1 = 2

Below is what our balanced chemical equation looks like.

As mentioned previous, placing the 2 in front of the molecule means multiply everything by 2. Such an example like this is really simple but provides a basic understanding of this process.

Conclusion

Chemical equations can be really fun to deal with once you understand how this works. In the beginning, it can be truly frustrating but perseverance will make the difference.

Physical & Chemical Changes in Chemistry

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In this post, we will focus most of our attention on physical changes in chemistry with a brief look at chemical changes.

Changes

Physical change is a change to a substance that does not alter the chemical composition. For example, boiling water is a physical change. Generally, physical changes are easy to reverse, such as when steam is cooled to become liquid water.

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Chemical change is a change that alters the chemical composition of a substance. An example would be various forms of cooking, such as frying potatoes to make french fries. Unlike physical changes, chemical changes are much harder to reverse. Just as it is impossible to turn french fries back into raw potatoes.

A specific type of physical change is called phase change. There are several different types of phase changes, as listed below.

  • melting
  • vaporizing
  • freezing
  • condensing
  • sublimation

Many of these are obvious, but they will be explained for clarity. Melting involves a substance moving from a solid to a liquid. Vaporizing takes place as a substance moves from liquid to gas. A substance that moves from a gas to a liquid is called condensing. Freezing is the process of a liquid becoming a solid. Sublimation is a solid moving straight to a gas.

The first four-phase changes are commonly seen in water. Ice melts to become liquid water, water boils/evaporates (vaporizes) to become steam. Water freezes to become ice; in the early morning, it is common in many places to see water on plants due to condensation. Sublimation is tricker to see on a day-to-day basis. The most common example involves carbon dioxide, aka dry ice, which is a favorite tool for Halloween. Other substances that sublimate include arsenic, iodine, and naphthalene (used for mothballs).

Phase changes are related to the kinetic theory of matter, which we will now turn our attention to.

Kinetic Theory of Matter

The kinetic theory of matter states that Molceults have space between them and are in constant random motion. We can say that the more heat, the faster the motion because more energy is present. For solid, the molecules can vibrate, but that is essentially it. All solids are vibrating, such as tables, chairs, desks, etc. However, the vibration is random, and thus the vibrations cancel each other.

Liquids can clearly move about, and this is why they cannot keep a single shape but is formed by their circumstances. This also applies to gasses. The real difference between the various phases is the space around molecules and the speed at which they are moving. When energy is added, molecules move apart and move faster. This explains a solid becoming a liquid and a liquid a gas.

Water breaks many rules in relation to the Kinetic theory of matter. When water freezes, instead of the molecules getting closer together, they actually push out and are thus less dense than water. This is one reason why ice floats and why you would find frozen ice on the top of a lake. The ice floats to the top, and by being on top, it insulates the animals inside the lake from the cold above.

Conclusion

Physical changes play a major role in all of our lives. The phase changes of water are used for various purposes in everyday life. It is beneficial to understand these concepts as they are so commonly encountered.

Lewis Structures with LaTeX VIDEO

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Lewis structures are used to illustrate the valence electrons of an atom. The video below explains how to make these diagrams using LaTeX. For chemistry students this is a great intro to using LaTeX for completing assignments.

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Dalton’s Atomic Theory

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John Dalton was an 18th-century scientist who made several significant contributions to his field. One of his most prominent works was his Atomic theory. Dalton’s Atomic theory is a major concept in the study of chemistry. In this post, we will look at this theory and share some of the misunderstandings that Dalton had at his time.

Atomic Theory

Dalton’s Atomic Theory has four propositions to it.

  1. All matter is made of atoms that cannot be divided or destroyed
  2. All atoms of an element are identical in all their properties
  3. Compounds are formed by a combo of two or more different kinds of atoms
  4. A chemical reaction is a rearrangement of the atoms in the substance

There is little to explain here. Part one states that atoms cannot be divided or destroyed. In other words, the atom is the fundamental unit of the universe. Part 2 states that all atoms are identical in their properties, which implies that every atom of an element has the same number of protons, neutrons, and electrons.

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The third component states that compounds are formed by two or more different atoms. For example, one compound would be H2O which is water. Since there are two elements in H2O, it meets the definition of a compound. We also call such a compound a molecule. Component four states that a chemical reaction is a rearrangement of the atoms in the substance. An example of this would be digestion which involves significant chemical changes to the food.

Problems with Dalton’s Theory

Despite the brilliance of Dalton’s theory, several problems have arisen as researchers have continued to explore the mysteries of chemistry. For example, the first proposition of Dalton states that atoms cannot be divided or destroyed. Both of these claims are false. We now know that atoms are made of protons, neutrons, and electrons. In addition, atoms can be destroyed, which happens at any nuclear power plant through fission. Nuclear fission involves neutrons hitting atoms which causes them to split.

Dalton was also incorrect regarding his second proposition about the same atoms having the same properties. With the discovery of the neutron, it became clear that atoms may have the same chemical properties but not the same physical properties. The reason for this is that having a different number of neutrons affects the atom’s weight. When atoms of the same element have different neutrons, we call these isotopes.

Conclusion

Dalton’s work in the study of atoms is something to be praised. It is understandable that perhaps he got some things wrong. The purpose of science is to grow and improve over time, and this means that sometimes great scientists are right, but they must also be wrong.

Terms Related to Matter

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Matter is the physical stuff that everything around us is generally made of. Trees, birds, water, etc., are all examples of matter. Since almost everything is considered matter, scientists have naturally found ways to classify matter to better understand it.

Types of Matter

One way matter is classified whether it is a pure substance or a mixture. A pure substance is a substance that has the same properties throughout out it. An example of a pure substance would be salt or sugar. Both of the substances are only made of salt or sugar, and the properties of these two substances are the same if you have one or the other in a sample.

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On the other hand, a mixture is a combination of two or more substances. For example, if you have salt and pepper inside the same shaker, this is a mixture. This is because separating the salt and the pepper from each other is possible. Separating pure substances is generally not possible physically. However, pure substances can further be broken down into elements and compounds.

Elements are fundamental substances that cannot be broken down into simpler substances. The periodic table contains all known elements. Examples include oxygen, sodium, carbon, etc. Compounds are pure substances that are made of two or more elements. Compound examples include salt, sugar, carbon dioxide, etc.

More on Mixtures

Returning to mixtures, there are two types of mixtures: homogenous and heterogeneous. Homogenous mixtures have the same composition throughout the sample. Examples include milk and sugar water. In both of these examples, the substances that make up the mixture are evenly spread throughout the sample.

Heterogeneous mixtures have different compositions in parts of the sample. A classic example of this is salad dressing. When salad dressing is allowed to sit, it separates clearly into the various substances/homogenous mixture that it is made up of. This is why salad dressing must be shaken before it is enjoyed.

Law of mass conservation

Antoine Lauren de Lavoisier developed the law of mass conservation, which states that in any chemical or physical process, the total mass of everything involved must remain the same. This means that if you start with 5 kg of wood and burn it, there will still be 5kg of matter in a different form. You might see a pile of ashes that weighs less but what happens is that some of the matter was converted to gases and smoke in the burning process. Essentially, matter can be created or destroyed but can only be converted or broken down.

Conclusion

No pun intended, but matter matters. For students, it is important to develop an understanding of concepts related to chemistry. Doing so may help at least some of them prepare for whatever occupation they may have in the future.